Genetic Diversity of Hemp Germplasm in Northern Thailand

Abstract

Cannabis sativa L., commonly known as hemp, is a plant native to Central Asia. It is well known for its cannabinoid compounds, which have significant potential for medical applications. Recognizing the economic and medical value of hemp, the Thai government has permitted its cultivation for commercial, medical, and research purposes. However, a comprehensive understanding of hemp genetics is crucial to support industry expansion and enhance future breeding programs. This study investigated the genetic diversity of 37 hemp accessions collected in northern Thailand, along with two reference varieties (RPF1 and RPF2). Using DArTSeq-based genotyping-by-sequencing and whole-genome sequencing technologies, we identified 3,609 single nucleotide polymorphisms (SNPs). STRUCTURE analysis, principal component analysis (PCA), and neighbor-joining analysis consistently identified three genetic clusters; however, these clusters did not correlate with geographical locations. Genetic differentiation among clusters was observed (fixation index, FST = 0.064-0.079; Nei’s coefficient of genetic differentiation, Nei’s GST = 0.058-0.078). Total genetic diversity estimated (expected heterozygosity, HE = 0.348; observed heterozygosity, HO = 0.092). Global inbreeding (FIT = 0.033) and molecular variance (4.83%) suggested low to moderate genetic differentiation, while the high inbreeding coefficient (FIS = 0.737) indicated substantial inbreeding within clusters. The genetic data from this study provide a resource for developing molecular markers to distinguish hemp varieties, supporting selective breeding efforts. These findings will contribute to improving agronomic traits, conserving genetic diversity, and ensuring the sustainable use of hemp genetic resources